Biotechnologies

Animals that glow in dark

noreply@blogger.com (Weng Wah - 荣华) — Sat, 05 Jan 2008 20:48:00 +0000

South Korea scientists have successfully cloned cats that glow in dark. It was announced last December.

This may be the fluffiest, freakiest thing since Alba, the green fluorescent bunny from artist Eduardo Kac.

South Korean scientists tinkering with fluorescence protein genes say they have bred white Turkish Angora cats to glow red under ultraviolet light.

The pair of cats cloned from a mother's altered skin cell are nearly a year old. The researchers told the AFP that their work could help unravel mysteries of some 250 genetic diseases suffered by both humans and cats. The findings also could be used to clone endangered tigers, leopards, and other animals, the report said.

However, it's unlikely that such psychedelic-looking cats would come to pet stores anytime soon. Debates about the ethics and safety of concocting cloned and transgenic animals continue to rage.

This is no longer a new to us. Amongst the animals that glow-in-darks using GFP technology are as below:

Pigs - Taiwan (Jan 2006)
National Taiwan University cloned 3 pigs which are green inside out inclusive their internal organs.

Rabbit (named Alba) - French 2001
Fluorescent jellyfish called Aequorea victoria gene (EGFP - enhanced Green Fluorescent Protein) was zygote microinjection into fertilized rabbit eggs.

Zebrafish - Japan 1997

Blast2GO

noreply@blogger.com (Weng Wah - 荣华) — Fri, 04 Jan 2008 05:06:00 +0000

If you intend to find a gene function from the BLAST results. You may try out Blast2GO. It is simple to use and short learning curve. Furthermore, i love the integrated interpro and KEGG pathway inference. You also will be able to classify your genes based on GO. Give it a try.

Welcoming 2008

noreply@blogger.com (Weng Wah - 荣华) — Tue, 01 Jan 2008 03:24:00 +0000

BLAT vs BLAST

noreply@blogger.com (Weng Wah - 荣华) — Fri, 07 Sep 2007 16:51:00 +0000

Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome. The index -- which uses less than a gigabyte of RAM -- consists of all non-overlapping 11-mers except for those heavily involved in repeats. This smaller size means that Blat is far more easily mirrored. Blat of DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or short sequence alignments.

On proteins, Blat uses 4-mers rather than 11-mers, finding protein sequences of 80% and greater similarity to the query of length 20+ amino acids. The protein index requires slightly more than 2 gigabytes of RAM. In practice -- due to sequence divergence rates over evolutionary time -- DNA Blat works well within humans and primates, while protein Blat continues to find good matches within terrestrial vertebrates and even earlier organisms for conserved proteins. Within humans, protein Blat gives a much better picture of gene families (paralogs) than DNA Blat. However, BLAST and psi-BLAST at NCBI can find much more remote matches.

From a practical standpoint, Blat has several advantages over BLAST:

* speed (no queues, response in seconds) at the price of lesser homology depth
* the ability to submit a long list of simultaneous queries in fasta format
* five convenient output sort options
* a direct link into the UCSC browser
* alignment block details in natural genomic order
* an option to launch the alignment later as part of a custom track

Blat is commonly used to look up the location of a sequence in the genome or determine the exon structure of an mRNA, but expert users can run large batch jobs and make internal parameter sensitivity changes by installing command line Blat on their own Linux server.

Genetic Engineering News

noreply@blogger.com (Weng Wah - 荣华) — Wed, 25 Oct 2006 16:10:00 +0000

The current issue of GEN is out. You may subcribe to Genetic Engineering News.
A very informative and resourceful site to keep us updated with the latest technologies.

Genetic Engineering News (GEN), the only high-frequency publication dedicated to biotech news, was introduced in 1981, as the first biotechnology trade publication. GEN is now the most widely read bionews publication worldwide.

Interesting Highlights:

Next Generation Sequencing

noreply@blogger.com (Weng Wah - 荣华) — Wed, 25 Oct 2006 14:53:00 +0000

454 Life Sciences Technologies

For the first time in nearly a decade there is a new choice in commercially available DNA-sequencing platforms. As a result there has been a flurry of development activity that promises to lead to other new platforms being generally available. This has energized the sequencing community and, more than ever before, encouraged new entrants into the field.

The achievement of the human genome project was entirely performed by fluorescent Sanger di-deoxyribonucleotide sequencing, which was almost exclusively provided by Applied Biosystems. Other vendors also supported fluorescent/Sanger-based methods, including Molecular Dynamics (GE Healthcare), Beckman Coulter, and LiCor Biosciences, but Applied Biosystem’s ABI 3700 was the workhorse for the first mammalian genome. As a consequence there are more AB machines in modern laboratories than any equivalent devices......

With the recent platform innovations, it will play a vital role in the discovery of new variations. The precise pathway to discover all human sequence variation is not yet clear but it is likely that methods other than fluorescent Sanger dideoxy sequencing will have prominent role.